Abstract 3270: The XernaTM TME Panel potentially predicts response to a combination of the TLR9 agonist vidutolimod and PD-1 inhibitor pembrolizumab in metastatic melanomas with prior anti-PD-1 treatment

• Published in: Cancer research (Chicago, Ill.) Ill.), 2023-04, Vol.83 (7_Supplement), p.3270-3270
• Main Authors: Uhlik, Mark T., Pointing, Daniel, Ausec, Luka, Stajdohar, Miha, Cvitkovic, Robert, Zganec, Matjaz, Iyer, Seema, Liu, Hong, Krieg, Art, Benjamin, Laura
• Format: Article
• Language: English
• ISSN: 1538-7445; 1538-7445
• DOI: 10.1158/1538-7445.AM2023-3270

Background: Few therapeutic options exist for anti-PD-1 refractory, metastatic melanoma patients, and today’s biomarkers are insufficient to aid in defining who should receive potential combinatorial immunotherapies. Results from a phase Ib, multicenter study (NCT02680184) showed that a combination of vidutolimod and pembrolizumab provided a best overall response of 23.5% in patients with metastatic or unresectable cutaneous melanoma who had received prior anti-PD-1 therapy. The Xerna™ TME Panel consists of an artificial neural net that utilizes the expression of ~100 genes involved in angiogenesis and tumor immune biologies to classify patient samples into one of four tumor microenvironment (TME) biomarker subtypes: Angiogenesis (A), Immune Active (IA), Immune Desert (ID), or Immune Suppressed (IS). We hypothesized that the IS subtype is predictive of vidutolimod + pembrolizumab benefit in this cohort compared to the other TME subtypes (A, IA, and ID). Methods: Total RNASeq was performed on FFPE biopsies collected from a subset of patients prior to therapy (N=38) and 2 weeks post-initiation of therapy (N=10). Gene expression data was analyzed using the Xerna TME Panel algorithm to assign a TME subtype. Correlational analyses between TME subtypes, response to therapy, and other hallmark gene signatures were performed. Results: Overall response rate in the pretreatment cohort available for biomarker analysis was 26%, comparable to the entire vidutolimod/pembrolizumab arm. The cohort had a skewed distribution of TME subtypes with high prevalence of IS (34%) and ID (45%), indicative of immune therapy-refractory biologies. An overall response of 54% was observed in the IS subtype, compared with 12% in the other subtypes combined. Comparison with other “hallmark” gene signatures confirmed enrichment of immune and angiogenesis biologies in the IS subtype, but none of these individual hallmark signatures were found to differentiate between responders and non-responders. The Xerna TME Panel demonstrated superior classification performance across all criteria compared to a baseline classifier, including accuracy (0.76 vs. 0.62), sensitivity (0.70 vs. 0.27) and specificity (0.79 vs. 0.74). Among matched post-treatment samples, 70% revealed a change in TME subtype compared to their pre-treatment status. Three of the post-treatment samples represented changes from an immune-low subtype to an immune-high subtype, including one complete responder with a pre-treatment ID